separate_quant_matrices: Separate a multiple-quantification matrix into single...

In ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Description

\lifecycle

maturing The function separates a single multi-quantification integration matrix, obtained via comparison_matrix, into single quantification matrices as a named list of tibbles.

Usage

separate_quant_matrices(
  x,
  fragmentEstimate = "fragmentEstimate",
  seqCount = "seqCount",
  barcodeCount = "barcodeCount",
  cellCount = "cellCount",
  ShsCount = "ShsCount"
)

Arguments

x	Single integration matrix with multiple quantification value columns, likely obtained via comparison_matrix.
fragmentEstimate	Name of the fragment estimate values column in input
seqCount	Name of the sequence count values column in input
barcodeCount	Name of the barcode count values column in input
cellCount	Name of the cell count values column in input
ShsCount	Name of the shs count values column in input

Value

A named list of tibbles, where names are quantification types

See Also

quantification_types

Other Analysis functions: CIS_grubbs(), comparison_matrix(), compute_abundance(), cumulative_count_union(), sample_statistics(), threshold_filter(), top_integrations()

Examples

op <- options("ISAnalytics.widgets" = FALSE)
path <- system.file("extdata", "ex_association_file.tsv",
    package = "ISAnalytics"
)
root_pth <- system.file("extdata", "fs.zip", package = "ISAnalytics")
root <- unzip_file_system(root_pth, "fs")
association_file <- import_association_file(path = path, root = root,
dates_format = "dmy")
matrices <- import_parallel_Vispa2Matrices_auto(
    association_file = association_file,
    quantification_type = c("seqCount", "fragmentEstimate"),
    matrix_type = "annotated", workers = 2, patterns = NULL,
    matching_opt = "ANY"
)
separated_matrix <- separate_quant_matrices(matrices)
options(op)

ISAnalytics documentation built on April 9, 2021, 6:01 p.m.